Hi everyone, for a metagenomic analysis i started with a long reads file (of a mixed bacterial culture containing, in theory, 2 bacteria) that i assembled with flye (in metagenomic mode) and finally binned with metabat2.

I got 2 bin, the problem is that one of them has a cumulative length of 3.9Mb, and it has been classified as a bacteria with a reference genome of circa 2.3-2.4Mb. i have tried to increase the specificity of metabat2 to reduce the false positive hits (if there were any) but the result is the same.

Why do i obtain a bin that exceeds in length the reference genome? in theory there aren't different strain of this bacterium in the culture. And there are methods to fix this problem?

Thanks for the reply